rs4233356

Positions:

• chr1-159783393-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.634 in 152,094 control chromosomes in the GnomAD database, including 30,758 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (30758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96354 AN: 151976 Hom.: 30729 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.634 AC: 96424 AN: 152094 Hom.: 30758 Cov.: 33 AF XY: 0.642 AC XY: 47728 AN XY: 74348

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.587

Alfa AF: 0.628 Hom.: 67902

Bravo AF: 0.623

Asia WGS AF: 0.684 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4233356; hg19: chr1-159753183;